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Updated: Sep 16, 2025
Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
Published on: July 6, 2022
Spatial Transcriptomics Unveils Regional Heterogeneity and Subclonal Dynamics in the Lung Adenocarcinoma
Haoyuan An1, Wei Fang2, Haiyan Chen3
1Department of Biomedical Engineering Institute, School of Control Science and Engineering, Shandong University, Jinan, Shandong, China.
Background And Objective:
Lung adenocarcinoma has high incidence and mortality rates. While single-cell transcriptomics reveals tumor cell heterogeneity, it lacks spatial detail, leaving the spatial dynamics and functional heterogeneity largely unexplored. This study aims to utilize spatial transcriptomics to provide a comprehensive cellular landscape of lung adenocarcinoma, addressing the limitations of single-cell analysis.
Methods:
Utilizing cell type-specific markers and spatial transcriptomics data derived from single-cell transcriptomic analysis, we performed cell deconvolution, assessed tissue preferences, constructed trajectories, and analyzed spot-spot interactions to create a comprehensive cellular landscape of lung adenocarcinoma.
Results:
We conducted unsupervised dimensionality reduction clustering on 125,203 single cells from single-cell transcriptomics, and used this data to deconvolute the cellular composition of each of the 3990 spots in a separately analyzed spatial transcriptomics sample. By constructing a trajectory from the tumor's periphery to its core, we discovered that pathways related to oxygen level responses were significantly upregulated, while immune response pathways were notably downregulated. Pseudotime analysis identified fibroblast areas closely associated with the tumor, with neighboring tumor areas exhibiting strong epithelial-mesenchymal transition and tumor migration characteristics, defined as the direction of tumor invasion. Further dimensionality reduction clustering within the tumor area differentiated six subgroups, each showing significant spatial and functional heterogeneity. Notably, the Ca_0 subgroup is closely linked to the tumor invasion process, whereas the Ca_1 subgroup is significantly associated with poor prognosis. Interaction analysis suggests that the Ca_1 subgroup may facilitate overall tumor progression by promoting angiogenesis and immune escape, rather than by directly participating in tumor invasion.
Conclusions:
This study provides an in-depth analysis of the spatial-functional heterogeneity in lung adenocarcinoma and its microenvironment, revealing four functionally heterogeneous groups with significant spatial and functional diversity within the tumor microenvironment. The study also identifies key areas and gene expression changes closely associated with tumor invasion and progression, highlighting critical aspects of tumor dynamics.
